No subject found

Hi trying to run the nextflow command, I used the bids validator tool and my datase is Bids-valid but I get this ‘No subject found’ error. I even tried to run it on a dataset on which I was able to run nextlow before (the folders are the same and it’s the same line of command I used before on that dataset), and I still get the same message. Any idea what else I should check? I tried the --input, --bids and --root options

ERROR nextflow.extension.DataflowHelper - @unknown
nextflow.exception.ProcessUnrecoverableException: Error ~ No subjects found. Please check the naming convention, your --input path or your BIDS folder.

Hello,

What are you trying to run? Can you point us to any online documentation?

Best,
Steven

Edit: I see from the tag that you are trying to run TractoFlow. What command are you using?

This:
nextflow run tractoflow/main.nf --bids data/ --dti_shells “0 1000” --fodf_shells “0 1000” -with-singularity /home/myenv/tractoflow/tractoflow_2.2.1_b9a527_2021-04-13.sif -resume

What are the contents of data/?

image

That looks like the folder name is data3, not data. Also, it might help to enter the full path to data3 In your tractorflow command.

Best,
Steven

Yes I did write data3/ in my script, I modify my line depending on which folder I work with and I also tried the full path. It finds the data or data3 folder but it says there are no subjects in it